Interactive Index
Every simulator, game, quiz and interactive figure in the course65 interactive pieces are linked from the fourteen week pages, scattered across a dozen directories of this site. This page gathers all of them in one place, with 12 more that are relevant but that no week page currently links. Several appear in more than one week — the FID demo turns up in Weeks 02, 03 and 11 — so the per-week counts below add up to more than 65. Search filters on title, description and week. Nothing here needs an install or a login; everything runs in the browser.
Week 01: Introduction & History4
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Neuroimaging Perspectives: Clinical vs. Research
Explore how clinical radiologists and neuroscientists interpret brain scans differently: qualitative PACS workstations and single-patient pathology vs. quantitative group-level statistics and automated volumetric analysis in research.
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Diagnostic Test & Confusion Matrix Calculator
Manipulate sensitivity, specificity, and disease prevalence to visualize true/false positives and confusion matrices, demonstrating how pre-test probability impacts clinical imaging biomarkers.
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Neuroimaging Dichotomous Key
Step through an interactive dichotomous key to differentiate neuroimaging modalities (CT, SPECT, PET, DSA, EEG, MEG, fMRI, structural MRI, fNIRS, and TCD) based on ionizing vs. non-ionizing radiation, tracers, electromagnetic sensors, and physical contrasts.
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Diagnostic Incoming Self-Assessment Quiz
A quick pre-assessment quiz covering core neuroimaging modalities, signal sources, and spatial/temporal tradeoffs to evaluate your baseline knowledge.
Week 02: Physical Principles of MRI9
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MRI Simulator: Scanner, Sequences, k-space & Spectroscopy
Write pulse sequences in a small language, image a brain or a test phantom on a schematic 3 T scanner, and watch k-space fill line by line as the hardware plays the sequence. Reconstruct the data several ways (filters, zero-filling, partial Fourier, SENSE, gridding), switch on artifacts that arise from their physical cause, and acquire a non-localised proton FID with water suppression and hands-on shimming. Thirteen guided lessons.
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Free Induction Decay (FID) & Spin Relaxation
Directly connects the 3D time evolution of precessing and dephasing proton moments to the voltage signal induced in an RF receiver coil via Faraday's Law. Features continuous longitudinal memory across pulses.
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Gradient Encoding Visualizer
Observe how linear magnetic field gradients make precession frequencies position-dependent, demonstrating slice selection (Gz), phase encoding (Gy), and frequency encoding readout (Gx).
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Pulse Sequence Timing Diagram
A dynamic pulse sequence diagram. Adjust TE to see the 180° refocusing pulse and echo move together; adjust TR to visualize scanner repetition intervals and phase-encode step increments.
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k-space Explorer
Vary the fraction of k-space kept to see how central k-space governs coarse contrast while peripheral k-space yields sharp edges, demonstrating Gibbs / truncation ringing.
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3D NMR Relaxation & Proton Dynamics
Explore Bloch equation proton spin dynamics in 3D. Manipulate static field strength ($B_0$), $T_1$ recovery, and $T_2$ decay in real-time. Trigger 90° and 180° RF excitation pulses to watch nutation, precession, and magnetization vector evolution.
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Interactive 2D FFT & K-Space Simulator
Draw spatial patterns or test presets (sine gratings, checkerboards, Gaussian blobs, edge filters) to see the instantaneous 2D Fourier transform magnitude spectrum with DC centering and log scaling.
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Adding Rotating Vectors: Chemical Shift
Add two precessing magnetisation vectors turning at different rates and watch the sum beat in and out of phase. Presets for fat and water at 1.5 T and 3 T show why abdominal protocols use particular echo times, and how two-point Dixon separation works.
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MRI Safety Course & Force Simulator
Examine the spatial fringe field of superconducting magnets with an interactive magnetic attraction force slider ($F \propto B^2$), review projectile safety, and complete the MRI Safety Certification Quiz.
Week 03: Structural MRI & Contrast10
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MRI Simulator: Scanner, Sequences, k-space & Spectroscopy
Write pulse sequences in a small language, image a brain or a test phantom on a schematic 3 T scanner, and watch k-space fill line by line as the hardware plays the sequence. Reconstruct the data several ways (filters, zero-filling, partial Fourier, SENSE, gridding), switch on artifacts that arise from their physical cause, and acquire a non-localised proton FID with water suppression and hands-on shimming. Thirteen guided lessons.
-
Free Induction Decay (FID) & Spin Relaxation
Directly connects the 3D time evolution of precessing and dephasing proton moments to the voltage signal induced in an RF receiver coil via Faraday's Law. Features continuous longitudinal memory across pulses.
-
Pulse Sequence Timing Diagram
A dynamic pulse sequence diagram. Adjust TE to see the 180° refocusing pulse and echo move together; adjust TR to visualize scanner repetition intervals and phase-encode step increments.
-
EPI Geometric Distortion & Susceptibility Dropout
Examine macroscopic magnetic susceptibility gradients at air-tissue interfaces (paranasal sinuses) that cause phase-encoding distortion and intra-voxel dephasing signal blackout.
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TR/TE Contrast Explorer
Manipulate TR and TE sliders to see real-time spin-echo signal calculations across four tissue types (White Matter, Gray Matter, CSF, and Fat), dynamically identifying T1-weighted, T2-weighted, and PD-weighted regimes.
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MRI Artifact Simulator
Introduce deliberate k-space and spatial distortions to inspect Chemical Shift (fat-water frequency displacement), Aliasing / Wrap-around (reduced FOV), and Motion Ghosting (phase-encode modulation) with variable severity.
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The Spin Echo & Echo Trains
Watch the isochromat phase fan open at $T_2^*$ and close again under each 180° refocusing pulse. Run a full CPMG train and see every echo peak land on the $T_2$ envelope regardless of shim quality, which is how a multi-echo sequence measures $T_2$.
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Ernst Angle Calculator
Calculate the optimal excitation flip angle $\alpha_E = \arccos(e^{-TR/T_1})$ to maximize steady-state signal amplitude for gradient echo sequences at short repetition times.
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Ferroquant: Iron & Hemorrhage Susceptibility Contrast
Understand how paramagnetic and diamagnetic iron states (oxyhemoglobin, deoxyhemoglobin, methemoglobin, hemosiderin) alter local magnetic fields and shorten $T_2^*$, with a case study on subdural hematoma aging.
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MRI Modality Card Game
Match magnet types, imaged organs, excitation, relaxation, spatial encoding and reconstruction, and clinical applications.
Week 04: Functional MRI (fMRI)7
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EPI Geometric Distortion & Susceptibility Dropout
Examine macroscopic magnetic susceptibility gradients at air-tissue interfaces (paranasal sinuses) that cause phase-encoding distortion and intra-voxel dephasing signal blackout.
-
fMRI GLM & Convolution Studio
Connect neural events to the BOLD time series by convolving stimulus boxcars with the canonical double-gamma HRF, observing how metabolic delays shape voxel signals.
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fMRI Preprocessing Pipeline Workbench
See what stands between a raw EPI time series and a usable statistical map. Head motion, interleaved slice timing, drift and physiological noise are applied to a synthetic run, and each correction stage can be switched on and off to watch the $t$-map respond.
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Interactive BOLD Signal (HRF) Simulator
Trigger a 1-second sensory stimulus to contrast instantaneous electrical neural spiking with the sluggish BOLD Hemodynamic Response Function (HRF) peaking 5–6 seconds later, accompanied by a dynamic cortical activation display.
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Local Field Potentials (LFP) vs. Spikes
Simulate 150 neurons to see how synchronized postsynaptic potentials (LFPs) create macro-signals that drive astrocytic signaling and metabolic blood flow changes far more strongly than sparse action potentials.
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Stochastic Leaky Integrate-and-Fire (LIF) Neuron
Examine the cellular electrophysiological threshold, ion pumping energy requirements, and spike generation that necessitate local hemodynamic overcompensation.
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Ferroquant: Iron & Hemorrhage Susceptibility Contrast
Understand how paramagnetic and diamagnetic iron states (oxyhemoglobin, deoxyhemoglobin, methemoglobin, hemosiderin) alter local magnetic fields and shorten $T_2^*$, with a case study on subdural hematoma aging.
Week 05: fMRI Experimental Design8
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MRI Artifact Simulator
Introduce deliberate k-space and spatial distortions to inspect Chemical Shift (fat-water frequency displacement), Aliasing / Wrap-around (reduced FOV), and Motion Ghosting (phase-encode modulation) with variable severity.
-
fMRI GLM & Convolution Studio
Connect neural events to the BOLD time series by convolving stimulus boxcars with the canonical double-gamma HRF, observing how metabolic delays shape voxel signals.
-
fMRI Preprocessing Pipeline Workbench
See what stands between a raw EPI time series and a usable statistical map. Head motion, interleaved slice timing, drift and physiological noise are applied to a synthetic run, and each correction stage can be switched on and off to watch the $t$-map respond.
-
Interactive BOLD Signal (HRF) Simulator
Trigger a 1-second sensory stimulus to contrast instantaneous electrical neural spiking with the sluggish BOLD Hemodynamic Response Function (HRF) peaking 5–6 seconds later, accompanied by a dynamic cortical activation display.
-
Whole-Brain Thresholding & Multiple Comparisons
A statistical map is thousands of tests, not one. Threshold the same $t$-map four ways side by side, calibrate the cluster-extent threshold against null data by Monte Carlo, and audit how often each method reports an activation in data that contains none.
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Group-Level Inference: Fixed vs. Random Effects
Decide how many participants to recruit and how long to scan each one. Monte Carlo power curves show when between-subject variability makes longer sessions pointless, and a validity audit shows why a fixed-effects group analysis cannot support a claim about people.
-
Flash-Lag Psychophysics Experiment
Experience a classic visual perception timing experiment that illustrates how behavioral psychophysics paradigms are parameterized and synchronized with scanner trigger pulses.
-
1D Waveform & Fourier Spectrum Synthesizer
Explore frequency decompositions and harmonic content to understand why scanner drift (<0.01 Hz) and cardiac/respiratory noise are addressed using high-pass filters and physiological regressors.
Week 06: Diffusion Tensor Imaging (DTI)4
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DTI Tensor & Tractography Explorer
Shape the diffusion tensor by its eigenvalues and watch the six Stejskal-Tanner gradient measurements it would produce, then seed deterministic streamlines into a synthetic corpus-callosum / corticospinal crossing. Tune the FA stopping threshold, turning-angle limit, step size, and Euler vs. Runge-Kutta integration to see tracts terminate at the intersection, and to see them jump bundles and fabricate a connection when the angle limit is relaxed.
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Structural Connectome Matrix & Graph Theory Studio
Construct an anatomical adjacency matrix from whole-brain streamline tractography. Compute characteristic path length, clustering coefficient, and small-worldness (σ), then simulate random axonal injury vs. targeted rich-club hub lesions to explore network resilience.
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Interactive Fractional Anisotropy (FA) Simulator
Adjust the FA slider from 0.0 to 0.95+ to observe how water diffusion transitions from an isotropic sphere (free fluid in CSF) to a highly constrained ellipsoid parallel to densely packed, myelinated axonal fiber bundles.
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129Xe Microstructural Diffusion Primer
Explore how restricted Brownian motion is quantified using Apparent Diffusion Coefficient (ADC) mapping to probe microscopic anatomical barriers.
Week 07: Positron Emission Tomography5
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PET Pharmacokinetics & Compartment Modeling Studio
Simulate dynamic tracer kinetics across vascular, free/non-specifically bound, and specifically trapped compartments using a 4th-order Runge-Kutta solver. Fit arterial input functions, compute Time-Activity Curves (TACs), and perform graphical Patlak ($K_i$) and Logan ($V_T$) linear analyses.
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PET Sinogram & Tomographic Reconstruction Workbench
Map positron annihilation coincidence lines of response into Radon sinograms. Invert the intrinsic $1/r$ backprojection blurring with Ram-Lak ramp and Hann filters, and run iterative Poisson MLEM with 511 keV tissue attenuation correction.
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Interactive PET Scanner Simulation
A Monte Carlo scanner: radiotracer decay, positron range, annihilation into antiparallel 511 keV photons, Compton scatter and attenuation, energy and coincidence timing windows, randoms and dead time, and live sinogram reconstruction by filtered backprojection or iterative MLEM with time-of-flight.
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X-Ray Water Radiolysis Simulator
Explore photoelectric absorption, Compton scattering, and radical generation during high-energy photon interactions in biological tissue.
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PET Modality Card Game
Assemble complete hands connecting radioisotopes ($^{18}\text{F}$, $^{11}\text{C}$, $^{15}\text{O}$, $^{13}\text{N}$), target organs, positron emission through coincidence detection to reconstruction, and clinical applications.
Week 08: Electroencephalography (EEG)7
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Local Field Potentials (LFP) vs. Spikes
Simulate 150 neurons to see how synchronized postsynaptic potentials (LFPs) create macro-signals that drive astrocytic signaling and metabolic blood flow changes far more strongly than sparse action potentials.
-
EEG Simulator: From Dipoles to ERPs
Describe a recording in a small language (cap, reference, sampling rate, filters and a stimulus timeline with trials and conditions), record it from dipole sources in a four-shell head, and switch blinks, eye movements, muscle, cardiac, line noise, drift, pops and a bad channel on and off. Then re-reference, filter with the distortions visible, remove ICA components checked against the ground truth, watch an ERP emerge as SNR grows with $\sqrt{N}$, and fit a dipole to see how noise, electrode count and depth make the inverse ambiguous.
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EEG Forward Model & Scalp Potential Mapper
Interact with a current dipole in a 3-shell concentric head model (brain, skull $\sigma_{ratio} \approx 1:80$, scalp). Observe how volume conduction and skull resistivity smear potentials across the scalp, and visualize isopotential voltage contours and 10-20 electrode readouts in real time.
-
EEG Inverse Problem & Source Localization Studio
Reconstruct cortical current dipoles from 16-channel scalp electric potentials. Compare unregularized pseudoinverse noise explosion against Tikhonov Minimum Norm Estimation (MNE), depth-weighted wMNE, and spatial LCMV beamforming.
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Interactive Multi-Channel EEG & Artifact Simulator
Switch between canonical brainwave bands (Delta, Theta, Alpha, Beta, Gamma) across Frontal (Fp1), Central (Cz), and Occipital (O1) channels. Test realistic artifact injection buttons for Eye Blinks (EOG) and Jaw Clenching (EMG).
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Hodgkin-Huxley Action Potential Simulator
Investigate the voltage-gated $Na^+$ and $K^+$ channel dynamics that govern neuronal excitability and establish the membrane potentials measured by electrophysiological tools.
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EEG Modality Card Game
Match electrode types, the alpha, beta, theta and delta bands, the acquisition-to-artifact-removal pipeline, and clinical and BCI applications.
Week 09: Magnetoencephalography (MEG)5
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MEG Simulator: From Dipoles to Source Estimates
Describe a recording in a small language (sensor array, sampling rate, filters, noise suppression and a stimulus timeline with trials and conditions) and record it from dipole sources in a spherical head with magnetometers, axial or planar gradiometers, or on-scalp OPMs. Compare the MEG field map with the EEG potential map of the same source to see the 90° rotation, the silence of radial and deep sources and the smearing of EEG by the skull. Switch environmental noise, line noise, the heart, blinks, muscle, dental work, SQUID jumps, a bad channel and head movement on and off, then the shielded room, gradiometers and reference sensors, SSP and SSS, filters, ICA and movement compensation. Watch an evoked field emerge as SNR grows with $\sqrt{N}$, coregister the head with an MRI, and compare dipole fitting, minimum norm and a beamformer on the same data.
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EEG vs. MEG: Radial vs. Tangential Dipole Sensitivity
Directly test the fundamental biophysical difference between EEG and MEG: rotate a current dipole along a cortical fold (gyral crown vs. sulcal bank) to observe why radial dipoles produce zero external magnetic flux ($B_r = 0$) while tangential dipoles generate robust dipolar magnetic fields.
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Interactive SQUID Magnetometer vs. Gradiometer Simulator
Experience why gradiometer configurations (two opposing coils) are critical for measuring femtotesla neural signals: observe how uniform ambient magnetic noise is subtracted out while near-field cortical dipole signals are preserved.
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Vector Field & Curl Explorer
Visualize vector fields and rotational curl ($\nabla \times \vec{B}$), reinforcing the right-hand rule and magnetic field lines generated by primary intracellular dendritic currents.
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MEG Modality Card Game
Match SQUID, OPM and gradiometer sensors, the brain rhythms, shielding, signal space separation and source localization, and presurgical language mapping.
Week 10: Functional NIRS (fNIRS)5
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fNIRS Simulator: From Photons to Haemoglobin
Describe a recording in a small language (sources, detectors and short-separation channels over a 10-20 position, wavelengths, sampling rate and a block or event-related timeline with conditions) and record it from a five-layer head with an adjustable cortical activation, a connected pair, an infant, a thick skull or dark hair. Watch photons form the banana and trade depth against light as the separation grows, pick wavelengths against the HbO, HbR and water spectra, and follow intensity to optical density to concentration through the modified Beer-Lambert law. Switch the heartbeat, breathing, Mayer waves, a task-evoked scalp response, motion, a loose optode and room light on and off, then check quality, correct motion, filter, regress out the short channels, and watch the response emerge in the block average and the GLM while a false scalp activation disappears. Also compares fNIRS with BOLD fMRI and shows how a high-density array becomes diffuse optical tomography.
-
fNIRS Modified Beer–Lambert Unmixer
Work through the full optical chain: pick two laser wavelengths against the measured HbO2 and HHb extinction spectra, build the Modified Beer-Lambert matrix from the source-detector separation and differential pathlength factors, then push a simulated hyperemic response forward into two attenuation traces and solve the 2x2 system back to concentrations. Choosing both wavelengths on the same side of the isosbestic point makes the matrix ill-conditioned and reproduces the classic HbO2/HHb crosstalk artifact.
-
fNIRS Photon Transport & Short-Channel Scalp Regression
Simulate photon packet scattering random walks through layered scalp, skull, and brain cortex. Test dual-distance optodes to see how short-channel (8 mm) regression strips away confounding systemic blood pressure Mayer waves (0.1 Hz) to isolate true cortical activation.
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Interactive fNIRS 'Banana Path' & Hemodynamic Simulator
Watch animated photons diffuse along the characteristic curved 'banana path' between emitter and detector optodes. Trigger cortical stimulation to observe concurrent tracking of oxygenated hemoglobin ($\text{HbO}$) surge and deoxygenated hemoglobin ($\text{HbR}$) decrease.
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fNIRS Modality Card Game
Match source, detector and short-separation optodes, the chromophores that absorb near-infrared light, the modified Beer-Lambert law through block averaging, and applications from infants to hyperscanning.
Week 11: Magnetic Resonance Spectroscopy5
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MRI Simulator: Scanner, Sequences, k-space & Spectroscopy
Write pulse sequences in a small language, image a brain or a test phantom on a schematic 3 T scanner, and watch k-space fill line by line as the hardware plays the sequence. Reconstruct the data several ways (filters, zero-filling, partial Fourier, SENSE, gridding), switch on artifacts that arise from their physical cause, and acquire a non-localised proton FID with water suppression and hands-on shimming. Thirteen guided lessons.
-
Free Induction Decay (FID) & Spin Relaxation
Directly connects the 3D time evolution of precessing and dephasing proton moments to the voltage signal induced in an RF receiver coil via Faraday's Law. Features continuous longitudinal memory across pulses.
-
MRS Metabolite Basis Set & LCModel Spectral Fitter
Deconstruct in-vivo $^1\text{H}$ MR spectra into basis spectra for NAA, Creatine, Choline, Myo-inositol, Glutamate, and Lactate. Explore B0 field dispersion (1.5T vs 3T vs 7T), shim linewidths, macromolecular baselines, and Cramer-Rao Lower Bounds (CRLB %SD) across clinical tumor, stroke, and dementia presets.
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Interactive MRS Analysis Pipeline & Spectrum Simulator
A complete in-browser spectroscopy workstation. Adjust coil thermal noise, toggle the broad macromolecule baseline, apply a 10,000:1 water suppression filter, tune exponential apodization/line broadening (SNR vs. resolution), test zero-filling, and apply zero- and first-order phase corrections.
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Hyperpolarized & Multinuclear MRS Primer Hub
Explore advanced spectroscopy protocols including dissolved-phase hyperpolarized Xenon-129 (129xe_dissolved.html), Carbon-13 metabolic flux (13c_liver.html), and jMRUI software workflows (jmrui.html).
Week 12: Multi-modal Integration5
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Interactive BOLD Signal (HRF) Simulator
Trigger a 1-second sensory stimulus to contrast instantaneous electrical neural spiking with the sluggish BOLD Hemodynamic Response Function (HRF) peaking 5–6 seconds later, accompanied by a dynamic cortical activation display.
-
Simultaneous EEG-fMRI Artifact Decontamination Workbench
Step through the complete artifact removal pipeline for simultaneous EEG-fMRI acquisitions: eliminate millivolt gradient switching artifacts via Average Artifact Subtraction (AAS), remove ballistocardiogram (BCG) pulsatile motion artifacts via Optimal Basis Sets (OBS/PCA), and recover microvolt sensory Event-Related Potentials.
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Multi-Modal Fusion & Representational Similarity Analysis (RSA)
Bridge millisecond EEG dynamics and millimeter fMRI spatial activations without forced source constraints. Track condition-by-condition Representational Dissimilarity Matrices (RDMs) across post-stimulus time to map the spatiotemporal hierarchy from V1 to LOC and FFA.
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Kalman Filter Sensor Fusion Simulator
Tune process noise $Q$ versus measurement noise $R$ to understand how state-space filters combine noisy multi-sensor streams into an optimal hidden state estimate.
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NBL 425 Modality Game Center
Play through all five modality games (MRI, PET, EEG, MEG, fNIRS) to synthesize physical principles, hardware components, and clinical strengths across modalities.
Week 13: Emerging Modalities4
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Interactive SQUID Magnetometer vs. Gradiometer Simulator
Experience why gradiometer configurations (two opposing coils) are critical for measuring femtotesla neural signals: observe how uniform ambient magnetic noise is subtracted out while near-field cortical dipole signals are preserved.
-
Optically Pumped Magnetometers (OPM) & Wearable MEG Studio
Compare room-temperature wearable OPM arrays against rigid cryogenic SQUID helmets. Test how eliminating the $25-35\text{ mm}$ vacuum dewar gap yields a $4-5\times$ boost in magnetic flux ($B \propto 1/r^2$), enables pediatric imaging, and allows natural head motion with active background nulling coils.
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Self-Organized Criticality & Scale-Free Dynamics
Simulate sandpile avalanche distributions and power-law scaling ($1/f$ noise) to examine modern theories of scale-free brain network organization.
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Hyperpolarized 129Xe Gas Imaging Primer
Explore optical pumping with rubidium vapor to hyperpolarize noble gas nuclei, producing NMR signal enhancements of >100,000-fold that overcome thermal Boltzmann limits.
Week 14: Future & Final Projects4
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Brain-Wide Association Studies (BWAS) Power & Replication Simulator
Simulate brain-behavior association studies across sample sizes from $N = 25$ to $N = 4,000$. Discover why modest true effects ($|r| \approx 0.10$) produce severe effect size inflation ($r_{\text{obs}} \approx 0.50$) in underpowered cohorts, and run 1,000-study Monte Carlo audits to see why thousands of scans are required for honest replication.
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Interactive Spike Sorting (MUA to SUA)
Experiment with unsupervised K-Means clustering in waveform feature space (amplitude vs. width) to isolate single units from multi-unit recordings, illustrating algorithmic classification in neuroscience.
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Neuroimaging Dichotomous Key
Step through an interactive dichotomous key to differentiate neuroimaging modalities (CT, SPECT, PET, DSA, EEG, MEG, fMRI, structural MRI, fNIRS, and TCD) based on ionizing vs. non-ionizing radiation, tracers, electromagnetic sensors, and physical contrasts.
-
NBL 425 Modality Game Center
Play through all five modality games (MRI, PET, EEG, MEG, fNIRS) to synthesize physical principles, hardware components, and clinical strengths across modalities.
Simulators50
-
1D Waveform & Fourier Spectrum Synthesizer
Explore frequency decompositions and harmonic content to understand why scanner drift (<0.01 Hz) and cardiac/respiratory noise are addressed using high-pass filters and physiological regressors.
-
3D NMR Relaxation & Proton Dynamics
Explore Bloch equation proton spin dynamics in 3D. Manipulate static field strength ($B_0$), $T_1$ recovery, and $T_2$ decay in real-time. Trigger 90° and 180° RF excitation pulses to watch nutation, precession, and magnetization vector evolution.
-
Adding Rotating Vectors: Chemical Shift
Add two precessing magnetisation vectors turning at different rates and watch the sum beat in and out of phase. Presets for fat and water at 1.5 T and 3 T show why abdominal protocols use particular echo times, and how two-point Dixon separation works.
-
Brain-Wide Association Studies (BWAS) Power & Replication Simulator
Simulate brain-behavior association studies across sample sizes from $N = 25$ to $N = 4,000$. Discover why modest true effects ($|r| \approx 0.10$) produce severe effect size inflation ($r_{\text{obs}} \approx 0.50$) in underpowered cohorts, and run 1,000-study Monte Carlo audits to see why thousands of scans are required for honest replication.
-
DTI Tensor & Tractography Explorer
Shape the diffusion tensor by its eigenvalues and watch the six Stejskal-Tanner gradient measurements it would produce, then seed deterministic streamlines into a synthetic corpus-callosum / corticospinal crossing. Tune the FA stopping threshold, turning-angle limit, step size, and Euler vs. Runge-Kutta integration to see tracts terminate at the intersection, and to see them jump bundles and fabricate a connection when the angle limit is relaxed.
-
EEG Forward Model & Scalp Potential Mapper
Interact with a current dipole in a 3-shell concentric head model (brain, skull $\sigma_{ratio} \approx 1:80$, scalp). Observe how volume conduction and skull resistivity smear potentials across the scalp, and visualize isopotential voltage contours and 10-20 electrode readouts in real time.
-
EEG Inverse Problem & Source Localization Studio
Reconstruct cortical current dipoles from 16-channel scalp electric potentials. Compare unregularized pseudoinverse noise explosion against Tikhonov Minimum Norm Estimation (MNE), depth-weighted wMNE, and spatial LCMV beamforming.
-
EEG Simulator: From Dipoles to ERPs
Describe a recording in a small language (cap, reference, sampling rate, filters and a stimulus timeline with trials and conditions), record it from dipole sources in a four-shell head, and switch blinks, eye movements, muscle, cardiac, line noise, drift, pops and a bad channel on and off. Then re-reference, filter with the distortions visible, remove ICA components checked against the ground truth, watch an ERP emerge as SNR grows with $\sqrt{N}$, and fit a dipole to see how noise, electrode count and depth make the inverse ambiguous.
-
EEG vs. MEG: Radial vs. Tangential Dipole Sensitivity
Directly test the fundamental biophysical difference between EEG and MEG: rotate a current dipole along a cortical fold (gyral crown vs. sulcal bank) to observe why radial dipoles produce zero external magnetic flux ($B_r = 0$) while tangential dipoles generate robust dipolar magnetic fields.
-
EPI Geometric Distortion & Susceptibility Dropout
Examine macroscopic magnetic susceptibility gradients at air-tissue interfaces (paranasal sinuses) that cause phase-encoding distortion and intra-voxel dephasing signal blackout.
-
Flash-Lag Psychophysics Experiment
Experience a classic visual perception timing experiment that illustrates how behavioral psychophysics paradigms are parameterized and synchronized with scanner trigger pulses.
-
fMRI GLM & Convolution Studio
Connect neural events to the BOLD time series by convolving stimulus boxcars with the canonical double-gamma HRF, observing how metabolic delays shape voxel signals.
-
fMRI Preprocessing Pipeline Workbench
See what stands between a raw EPI time series and a usable statistical map. Head motion, interleaved slice timing, drift and physiological noise are applied to a synthetic run, and each correction stage can be switched on and off to watch the $t$-map respond.
-
fNIRS Modified Beer–Lambert Unmixer
Work through the full optical chain: pick two laser wavelengths against the measured HbO2 and HHb extinction spectra, build the Modified Beer-Lambert matrix from the source-detector separation and differential pathlength factors, then push a simulated hyperemic response forward into two attenuation traces and solve the 2x2 system back to concentrations. Choosing both wavelengths on the same side of the isosbestic point makes the matrix ill-conditioned and reproduces the classic HbO2/HHb crosstalk artifact.
-
fNIRS Photon Transport & Short-Channel Scalp Regression
Simulate photon packet scattering random walks through layered scalp, skull, and brain cortex. Test dual-distance optodes to see how short-channel (8 mm) regression strips away confounding systemic blood pressure Mayer waves (0.1 Hz) to isolate true cortical activation.
-
fNIRS Simulator: From Photons to Haemoglobin
Describe a recording in a small language (sources, detectors and short-separation channels over a 10-20 position, wavelengths, sampling rate and a block or event-related timeline with conditions) and record it from a five-layer head with an adjustable cortical activation, a connected pair, an infant, a thick skull or dark hair. Watch photons form the banana and trade depth against light as the separation grows, pick wavelengths against the HbO, HbR and water spectra, and follow intensity to optical density to concentration through the modified Beer-Lambert law. Switch the heartbeat, breathing, Mayer waves, a task-evoked scalp response, motion, a loose optode and room light on and off, then check quality, correct motion, filter, regress out the short channels, and watch the response emerge in the block average and the GLM while a false scalp activation disappears. Also compares fNIRS with BOLD fMRI and shows how a high-density array becomes diffuse optical tomography.
-
Free Induction Decay (FID) & Spin Relaxation
Directly connects the 3D time evolution of precessing and dephasing proton moments to the voltage signal induced in an RF receiver coil via Faraday's Law. Features continuous longitudinal memory across pulses.
-
Gradient Encoding Visualizer
Observe how linear magnetic field gradients make precession frequencies position-dependent, demonstrating slice selection (Gz), phase encoding (Gy), and frequency encoding readout (Gx).
-
Group-Level Inference: Fixed vs. Random Effects
Decide how many participants to recruit and how long to scan each one. Monte Carlo power curves show when between-subject variability makes longer sessions pointless, and a validity audit shows why a fixed-effects group analysis cannot support a claim about people.
-
Hodgkin-Huxley Action Potential Simulator
Investigate the voltage-gated $Na^+$ and $K^+$ channel dynamics that govern neuronal excitability and establish the membrane potentials measured by electrophysiological tools.
-
Interactive 2D FFT & K-Space Simulator
Draw spatial patterns or test presets (sine gratings, checkerboards, Gaussian blobs, edge filters) to see the instantaneous 2D Fourier transform magnitude spectrum with DC centering and log scaling.
-
Interactive BOLD Signal (HRF) Simulator
Trigger a 1-second sensory stimulus to contrast instantaneous electrical neural spiking with the sluggish BOLD Hemodynamic Response Function (HRF) peaking 5–6 seconds later, accompanied by a dynamic cortical activation display.
-
Interactive fNIRS 'Banana Path' & Hemodynamic Simulator
Watch animated photons diffuse along the characteristic curved 'banana path' between emitter and detector optodes. Trigger cortical stimulation to observe concurrent tracking of oxygenated hemoglobin ($\text{HbO}$) surge and deoxygenated hemoglobin ($\text{HbR}$) decrease.
-
Interactive Fractional Anisotropy (FA) Simulator
Adjust the FA slider from 0.0 to 0.95+ to observe how water diffusion transitions from an isotropic sphere (free fluid in CSF) to a highly constrained ellipsoid parallel to densely packed, myelinated axonal fiber bundles.
-
Interactive MRS Analysis Pipeline & Spectrum Simulator
A complete in-browser spectroscopy workstation. Adjust coil thermal noise, toggle the broad macromolecule baseline, apply a 10,000:1 water suppression filter, tune exponential apodization/line broadening (SNR vs. resolution), test zero-filling, and apply zero- and first-order phase corrections.
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Interactive Multi-Channel EEG & Artifact Simulator
Switch between canonical brainwave bands (Delta, Theta, Alpha, Beta, Gamma) across Frontal (Fp1), Central (Cz), and Occipital (O1) channels. Test realistic artifact injection buttons for Eye Blinks (EOG) and Jaw Clenching (EMG).
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Interactive PET Scanner Simulation
A Monte Carlo scanner: radiotracer decay, positron range, annihilation into antiparallel 511 keV photons, Compton scatter and attenuation, energy and coincidence timing windows, randoms and dead time, and live sinogram reconstruction by filtered backprojection or iterative MLEM with time-of-flight.
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Interactive Spike Sorting (MUA to SUA)
Experiment with unsupervised K-Means clustering in waveform feature space (amplitude vs. width) to isolate single units from multi-unit recordings, illustrating algorithmic classification in neuroscience.
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Interactive SQUID Magnetometer vs. Gradiometer Simulator
Experience why gradiometer configurations (two opposing coils) are critical for measuring femtotesla neural signals: observe how uniform ambient magnetic noise is subtracted out while near-field cortical dipole signals are preserved.
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k-space Explorer
Vary the fraction of k-space kept to see how central k-space governs coarse contrast while peripheral k-space yields sharp edges, demonstrating Gibbs / truncation ringing.
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Kalman Filter Sensor Fusion Simulator
Tune process noise $Q$ versus measurement noise $R$ to understand how state-space filters combine noisy multi-sensor streams into an optimal hidden state estimate.
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Local Field Potentials (LFP) vs. Spikes
Simulate 150 neurons to see how synchronized postsynaptic potentials (LFPs) create macro-signals that drive astrocytic signaling and metabolic blood flow changes far more strongly than sparse action potentials.
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MEG Simulator: From Dipoles to Source Estimates
Describe a recording in a small language (sensor array, sampling rate, filters, noise suppression and a stimulus timeline with trials and conditions) and record it from dipole sources in a spherical head with magnetometers, axial or planar gradiometers, or on-scalp OPMs. Compare the MEG field map with the EEG potential map of the same source to see the 90° rotation, the silence of radial and deep sources and the smearing of EEG by the skull. Switch environmental noise, line noise, the heart, blinks, muscle, dental work, SQUID jumps, a bad channel and head movement on and off, then the shielded room, gradiometers and reference sensors, SSP and SSS, filters, ICA and movement compensation. Watch an evoked field emerge as SNR grows with $\sqrt{N}$, coregister the head with an MRI, and compare dipole fitting, minimum norm and a beamformer on the same data.
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MRI Artifact Simulator
Introduce deliberate k-space and spatial distortions to inspect Chemical Shift (fat-water frequency displacement), Aliasing / Wrap-around (reduced FOV), and Motion Ghosting (phase-encode modulation) with variable severity.
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MRI Simulator: Scanner, Sequences, k-space & Spectroscopy
Write pulse sequences in a small language, image a brain or a test phantom on a schematic 3 T scanner, and watch k-space fill line by line as the hardware plays the sequence. Reconstruct the data several ways (filters, zero-filling, partial Fourier, SENSE, gridding), switch on artifacts that arise from their physical cause, and acquire a non-localised proton FID with water suppression and hands-on shimming. Thirteen guided lessons.
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MRS Metabolite Basis Set & LCModel Spectral Fitter
Deconstruct in-vivo $^1\text{H}$ MR spectra into basis spectra for NAA, Creatine, Choline, Myo-inositol, Glutamate, and Lactate. Explore B0 field dispersion (1.5T vs 3T vs 7T), shim linewidths, macromolecular baselines, and Cramer-Rao Lower Bounds (CRLB %SD) across clinical tumor, stroke, and dementia presets.
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Multi-Modal Fusion & Representational Similarity Analysis (RSA)
Bridge millisecond EEG dynamics and millimeter fMRI spatial activations without forced source constraints. Track condition-by-condition Representational Dissimilarity Matrices (RDMs) across post-stimulus time to map the spatiotemporal hierarchy from V1 to LOC and FFA.
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Optically Pumped Magnetometers (OPM) & Wearable MEG Studio
Compare room-temperature wearable OPM arrays against rigid cryogenic SQUID helmets. Test how eliminating the $25-35\text{ mm}$ vacuum dewar gap yields a $4-5\times$ boost in magnetic flux ($B \propto 1/r^2$), enables pediatric imaging, and allows natural head motion with active background nulling coils.
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PET Pharmacokinetics & Compartment Modeling Studio
Simulate dynamic tracer kinetics across vascular, free/non-specifically bound, and specifically trapped compartments using a 4th-order Runge-Kutta solver. Fit arterial input functions, compute Time-Activity Curves (TACs), and perform graphical Patlak ($K_i$) and Logan ($V_T$) linear analyses.
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PET Sinogram & Tomographic Reconstruction Workbench
Map positron annihilation coincidence lines of response into Radon sinograms. Invert the intrinsic $1/r$ backprojection blurring with Ram-Lak ramp and Hann filters, and run iterative Poisson MLEM with 511 keV tissue attenuation correction.
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Pulse Sequence Timing Diagram
A dynamic pulse sequence diagram. Adjust TE to see the 180° refocusing pulse and echo move together; adjust TR to visualize scanner repetition intervals and phase-encode step increments.
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Self-Organized Criticality & Scale-Free Dynamics
Simulate sandpile avalanche distributions and power-law scaling ($1/f$ noise) to examine modern theories of scale-free brain network organization.
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Simultaneous EEG-fMRI Artifact Decontamination Workbench
Step through the complete artifact removal pipeline for simultaneous EEG-fMRI acquisitions: eliminate millivolt gradient switching artifacts via Average Artifact Subtraction (AAS), remove ballistocardiogram (BCG) pulsatile motion artifacts via Optimal Basis Sets (OBS/PCA), and recover microvolt sensory Event-Related Potentials.
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Stochastic Leaky Integrate-and-Fire (LIF) Neuron
Examine the cellular electrophysiological threshold, ion pumping energy requirements, and spike generation that necessitate local hemodynamic overcompensation.
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Structural Connectome Matrix & Graph Theory Studio
Construct an anatomical adjacency matrix from whole-brain streamline tractography. Compute characteristic path length, clustering coefficient, and small-worldness (σ), then simulate random axonal injury vs. targeted rich-club hub lesions to explore network resilience.
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The Spin Echo & Echo Trains
Watch the isochromat phase fan open at $T_2^*$ and close again under each 180° refocusing pulse. Run a full CPMG train and see every echo peak land on the $T_2$ envelope regardless of shim quality, which is how a multi-echo sequence measures $T_2$.
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TR/TE Contrast Explorer
Manipulate TR and TE sliders to see real-time spin-echo signal calculations across four tissue types (White Matter, Gray Matter, CSF, and Fat), dynamically identifying T1-weighted, T2-weighted, and PD-weighted regimes.
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Vector Field & Curl Explorer
Visualize vector fields and rotational curl ($\nabla \times \vec{B}$), reinforcing the right-hand rule and magnetic field lines generated by primary intracellular dendritic currents.
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Whole-Brain Thresholding & Multiple Comparisons
A statistical map is thousands of tests, not one. Threshold the same $t$-map four ways side by side, calibrate the cluster-extent threshold against null data by Monte Carlo, and audit how often each method reports an activation in data that contains none.
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X-Ray Water Radiolysis Simulator
Explore photoelectric absorption, Compton scattering, and radical generation during high-energy photon interactions in biological tissue.
Tool & Primers8
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129Xe Microstructural Diffusion Primer
Explore how restricted Brownian motion is quantified using Apparent Diffusion Coefficient (ADC) mapping to probe microscopic anatomical barriers.
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Diagnostic Test & Confusion Matrix Calculator
Manipulate sensitivity, specificity, and disease prevalence to visualize true/false positives and confusion matrices, demonstrating how pre-test probability impacts clinical imaging biomarkers.
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Ernst Angle Calculator
Calculate the optimal excitation flip angle $\alpha_E = \arccos(e^{-TR/T_1})$ to maximize steady-state signal amplitude for gradient echo sequences at short repetition times.
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Ferroquant: Iron & Hemorrhage Susceptibility Contrast
Understand how paramagnetic and diamagnetic iron states (oxyhemoglobin, deoxyhemoglobin, methemoglobin, hemosiderin) alter local magnetic fields and shorten $T_2^*$, with a case study on subdural hematoma aging.
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Hyperpolarized & Multinuclear MRS Primer Hub
Explore advanced spectroscopy protocols including dissolved-phase hyperpolarized Xenon-129 (129xe_dissolved.html), Carbon-13 metabolic flux (13c_liver.html), and jMRUI software workflows (jmrui.html).
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Hyperpolarized 129Xe Gas Imaging Primer
Explore optical pumping with rubidium vapor to hyperpolarize noble gas nuclei, producing NMR signal enhancements of >100,000-fold that overcome thermal Boltzmann limits.
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MRI Safety Course & Force Simulator
Examine the spatial fringe field of superconducting magnets with an interactive magnetic attraction force slider ($F \propto B^2$), review projectile safety, and complete the MRI Safety Certification Quiz.
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Neuroimaging Perspectives: Clinical vs. Research
Explore how clinical radiologists and neuroscientists interpret brain scans differently: qualitative PACS workstations and single-patient pathology vs. quantitative group-level statistics and automated volumetric analysis in research.
Assessments2
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Diagnostic Incoming Self-Assessment Quiz
A quick pre-assessment quiz covering core neuroimaging modalities, signal sources, and spatial/temporal tradeoffs to evaluate your baseline knowledge.
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Neuroimaging Dichotomous Key
Step through an interactive dichotomous key to differentiate neuroimaging modalities (CT, SPECT, PET, DSA, EEG, MEG, fMRI, structural MRI, fNIRS, and TCD) based on ionizing vs. non-ionizing radiation, tracers, electromagnetic sensors, and physical contrasts.
Games6
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EEG Modality Card Game
Match electrode types, the alpha, beta, theta and delta bands, the acquisition-to-artifact-removal pipeline, and clinical and BCI applications.
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MEG Modality Card Game
Match SQUID, OPM and gradiometer sensors, the brain rhythms, shielding, signal space separation and source localization, and presurgical language mapping.
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fNIRS Modality Card Game
Match source, detector and short-separation optodes, the chromophores that absorb near-infrared light, the modified Beer-Lambert law through block averaging, and applications from infants to hyperscanning.
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MRI Modality Card Game
Match magnet types, imaged organs, excitation, relaxation, spatial encoding and reconstruction, and clinical applications.
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NBL 425 Modality Game Center
Play through all five modality games (MRI, PET, EEG, MEG, fNIRS) to synthesize physical principles, hardware components, and clinical strengths across modalities.
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PET Modality Card Game
Assemble complete hands connecting radioisotopes ($^{18}\text{F}$, $^{11}\text{C}$, $^{15}\text{O}$, $^{13}\text{N}$), target organs, positron emission through coincidence detection to reconstruction, and clinical applications.
Relevant but not yet on a week page12
These live on the site and bear on the course, but no week page links them. Worth either promoting onto the week they belong to or leaving here as optional depth. The week tag on each is my suggestion, not an existing link.
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Spin Echo Dephasing & Rephasing I (Grid)
The initial grid version of the dephasing and rephasing demo without the net sum vector. Week 03 links version II.
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Magnetic Domain Simulator
Domains aligning and reorienting under an applied field, behind the shim and fringe-field behaviour of a superconducting magnet.
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MRI Safety Certification Quiz
The safety quiz on its own, separate from the course module it is embedded in.
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Biophysical Contrast Simulation Sandbox
Sweeps tissue parameters across several contrast mechanisms in one place. Built for IDNE 701, but the physics is the same as Week 03.
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A Periodic Chart for Magnetic Resonance
Every NMR-active nucleus with its spin, gyromagnetic ratio, and natural abundance, which is the table you actually need when planning a multinuclear study.
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Vector Field Explorer
A second take on field visualisation alongside the curl plot used in Week 09.
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Fourier Analysis by Epicycles
Builds an arbitrary waveform out of rotating phasors, which is the same idea as filling k-space one spatial frequency at a time. From the mathematics series under garrity/.
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Cellular Automata: Game of Life
Local rules producing global structure. Sits with the self-organised criticality material in Week 13.
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Cellular Automata on Directed Graphs
Automata on an arbitrary graph rather than a grid, which is closer to how network models of cortex behave.
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Flocking and Collective Dynamics
Three local rules producing coherent group motion, another view of the emergence theme in Week 13.
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Hebbian Learning Demo
Weight change driven by correlated activity, companion to the leaky integrate-and-fire neuron in Week 04.
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NeuroSweep: Neural Array Sweep
Minesweeper reskinned onto an electrode array. Inference from sparse local evidence, which is a fair caricature of source localisation.